DOI QR코드

DOI QR Code

The gene repertoire of Pythium porphyrae (Oomycota) suggests an adapted plant pathogen tackling red algae

  • Badis, Yacine (The Scottish Association for Marine Science, Scottish Marine Institute) ;
  • Han, Jong Won (National Marine Biodiversity Institute of Korea) ;
  • Klochkova, Tatyana A. (Kamchatka State Technical University, Petropavlovsk-Kamchatsky) ;
  • Gachon, Claire M.M. (The Scottish Association for Marine Science, Scottish Marine Institute) ;
  • Kim, Gwang Hoon (National Marine Biodiversity Institute of Korea)
  • Received : 2020.01.30
  • Accepted : 2020.06.04
  • Published : 2020.06.15

Abstract

Pythium porphyrae is responsible for devastating outbreaks in seaweed farms of Pyropia, the most valuable cultivated seaweed worldwide. While the genus Pythium contains many well studied pathogens, the genome of P. porphyrae has yet to be sequenced. Here we report the first available gene repertoire of P. porphyrae and a preliminary analysis of pathogenicity-related genes. Using ab initio detection strategies, similarity based and manual annotation, we found that the P. porphyrae gene repertoire is similar to classical phytopathogenic Pythium species. This includes the absence of expanded RxLR effector family and the detection of classical pathogenicity-related genes like crinklers, glycoside hydrolases, cellulose-binding elicitor lectin-like proteins and elicitins. We additionally compared this dataset to the proteomes of 8 selected Pythium species. While 34% of the predicted proteome appeared specific to P. porphyrae, we could not attribute specific enzymes to the degradation of red algal biomass. Conversely, we detected several cellulases and a cutinase conserved with plant-pathogenic Pythium species. Together with the recent report of P. porphyrae triggering disease symptoms on several plant species in lab-controlled conditions, our findings add weight to the hypothesis that P. porphyrae is a reformed plant pathogen.

Keywords

References

  1. Adhikari, B. N., Hamilton, J. P., Zerillo, M. M., Tisserat, N., Levesque, C. A. & Buell, C. R. 2013. Comparative genomics reveals insight into virulence strategies of plant pathogenic oomycetes. PLoS ONE 8:e75072. https://doi.org/10.1371/journal.pone.0075072
  2. Ah-Fong, A. M. V., Shrivastava, J. & Judelson, H. S. 2017. Lifestyle, gene gain and loss, and transcriptional remodeling cause divergence in the transcriptomes of Phytophthora infestans and Pythium ultimum during potato tuber colonization. BMC Genomics 18:764. https://doi.org/10.1186/s12864-017-4151-2
  3. Arasaki, S., Akino, K. & Tomiyama, T. 1968. A comparison of some physiological aspects in a marine Pythium on the host and on the artificial medium. Bull. Misaki Mar. Biol. Inst. Kyoto Univ. 12:203-206.
  4. Ascunce, M. S., Huguet-Tapia, J. C., Ortiz-Urquiza, A., Keyhani, N. O., Braun, E. L. & Goss, E. M. 2017. Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage. Mol. Phylogenet. Evol. 114:199-211. https://doi.org/10.1016/j.ympev.2017.06.013
  5. Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W. & Noble, W. S. 2009. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 37:W202-W208. https://doi.org/10.1093/nar/gkp335
  6. Berger, H., Yacoub, A., Gerbore, J., Grizard, D., Rey, P., Sessitsch, A. & Compant, S. 2016. Draft genome sequence of biocontrol agent Pythium oligandrum strain Po37, an Ooomycota. Genome Announc. 4:e00215-16.
  7. Conesa, A. & Gotz, S. 2008. Blast2GO: a comprehensive suite for functional analysis in plant genomics. Int. J. Plant Genomics 2008:619832.
  8. Contreras-Moreira, B. & Vinuesa, P. 2013. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl. Environ. Microbiol. 79:7696-7701. https://doi.org/10.1128/AEM.02411-13
  9. de Cock, A. W. A. M., Lodhi, A. M., Rintoul, T. L., Bala, K., Robideau, G. P., Abad, Z. G., Coffey, M. D., Shahzad, S. & Levesque, C. A. 2015. Phytopythium: molecular phylogeny and systematics. Persoonia 34:25-39. https://doi.org/10.3767/003158515X685382
  10. Demchak, B., Hull, T., Reich, M., Liefeld, T., Smoot, M., Ideker, T. & Mesirov, J. P. 2014. Cytoscape: the network visualization tool for GenomeSpace workflows. F1000Res. 3:151. https://doi.org/10.12688/f1000research.4492.2
  11. Eddy, S. R. 2011. Accelerated profile HMM searches. PLoS Comput. Biol. 7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195
  12. Ellis, J. G. & Dodds, P. N. 2011. Showdown at the RXLR motif: serious differences of opinion in how effector proteins from filamentous eukaryotic pathogens enter plant cells. Proc. Natl. Acad. Sci. U. S. A. 108:14381-14382. https://doi.org/10.1073/pnas.1111668108
  13. Enright, A. J., Van Dongen, S. & Ouzounis, C. A. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30:1575-1584. https://doi.org/10.1093/nar/30.7.1575
  14. Fu, X. T. & Kim, S. M. 2010. Agarase: review of major sources, categories, purification method, enzyme characteristics and applications. Mar. Drugs 8:200-218. https://doi.org/10.3390/md8010200
  15. Gachon, C. M. M., Sime-Ngando, T., Strittmatter, M., Chambouvet, A. & Kim, G. H. 2010. Algal diseases: spotlight on a black box. Trends Plant Sci. 15:633-640. https://doi.org/10.1016/j.tplants.2010.08.005
  16. Gerlt, J. A., Bouvier, J. T., Davidson, D. B., Imker, H. J., Sadkhin, B., Slater, D. R. & Whalen, K. L. 2015. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): a web tool for generating protein sequence similarity networks. Biochim. Biophys. Acta 1854:1019-1037. https://doi.org/10.1016/j.bbapap.2015.04.015
  17. Gschloessl, B., Guermeur, Y. & Cock, J. M. 2008. HECTAR: a method to predict subcellular targeting in heterokonts. BMC Bioinformatics 9:393. https://doi.org/10.1186/1471-2105-9-393
  18. Haas, B. J., Kamoun, S., Zody, M. C., Jiang, R. H. Y., Handsaker, R. E., Cano, L. M., Grabherr, M., Kodira, C. D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T. O., Ah-Fong, A. M. V., Alvarado, L., Anderson, V. L., Armstrong, M. R., Avrova, A., Baxter, L., Beynon, J., Boevink, P. C., Bollmann, S. R., Bos, J. I. B., Bulone, V., Cai, G., Cakir, C., Carrington, J. C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M. A., Fugelstad, J., Gilroy, E. M., Gnerre, S., Green, P. J., Grenville-Briggs, L. J., Griffith, J., Grünwald, N. J., Horn, K., Horner, N. R., Hu, C. -H., Huitema, E., Jeong, D. -H., Jones, A. M. E., Jones, J. D. G., Jones, R. W., Karlsson, E. K., Kunjeti, S. G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M. C., McDonald, H., McWalters, J., Meijer, H. J. G., Morgan, W., Morris, P. F., Munro, C. A., O'Neill, K., Ospina-Giraldo, M., Pinzón, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D. C., Schumann, U. D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D. J., Sykes, S., Thines, M., van de Vondervoort, P. J. I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B. C., van West, P., Ristaino, J., Govers, F., Birch, P. R. J., Whisson, S. C., Judelson, H. S. & Nusbaum, C. 2009. Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398. https://doi.org/10.1038/nature08358
  19. Horner, N. R., Grenville-Briggs, L. J. & Van West, P. 2012. The oomycete Pythium oligandrum expresses putative effectors during mycoparasitism of Phytophthora infestans and is amenable to transformation. Fungal Biol. 116:24-41. https://doi.org/10.1016/j.funbio.2011.09.004
  20. Jiang, R. H. Y. & Tyler, B. M. 2012. Mechanisms and evolution of virulence in oomycetes. Annu. Rev. Phytopathol. 50:295-318. https://doi.org/10.1146/annurev-phyto-081211-172912
  21. Kim, G. H., Moon, K. -H., Kim, J. -Y., Shim, J. & Klochkova, T. A. 2014. A revaluation of algal diseases in Korean Pyropia (Porphyra) sea farms and their economic impact. Algae 29:249-265. https://doi.org/10.4490/algae.2014.29.4.249
  22. Klochkova, T. A., Jung, S. & Kim, G. -H. 2016. Host range and salinity tolerance of Pythium porphyrae may indicate its terrestrial origin. J. Appl. Phycol. 29:371-379. https://doi.org/10.1007/s10811-016-0947-8
  23. Klochkova, T. A., Shim, J. B., Hwang, M. S. & Kim, G. H. 2012. Host-parasite interactions and host species susceptibility of the marine oomycete parasite, Olpidiopsis sp., from Korea that infects red algae. J. Appl. Phycol. 24:135-144. https://doi.org/10.1007/s10811-011-9661-8
  24. Krajaejun, T., Khositnithikul, R., Lerksuthirat, T., Lowhnoo, T., Rujirawat, T., Petchthong, T., Yingyong, W., Suriyaphol, P., Smittipat, N., Juthayothin, T., Phuntumart, V. & Sullivan, T. D. 2011. Expressed sequence tags reveal genetic diversity and putative virulence factors of the pathogenic oomycete Pythium insidiosum. Fungal Biol. 115:683-696. https://doi.org/10.1016/j.funbio.2011.05.001
  25. Krajaejun, T., Kittichotirat, W., Patumcharoenpol, P., Rujirawat, T., Lohnoo, T. & Yingyong, W. 2018. Data on whole genome sequencing of the oomycete Pythium insidiosum strain CBS 101555 from a horse with pythiosis in Brazil. BMC Res. Notes 11:880. https://doi.org/10.1186/s13104-018-3968-3
  26. Kushwaha, S. K., Vetukuri, R. R. & Grenville-Briggs, L. J. 2017. Draft genome sequence of the mycoparasitic oomycete Pythium oligandrum strain CBS 530.74. Genome Announc. 5:e00346-17.
  27. Lee, S. J., Hwang, M. S., Park, M. A., Baek, J. M., Ha, D. -S., Lee, J. E. & Lee, S. -R. 2015. Molecular identification of the algal pathogen Pythium chondricola (Oomycetes) from Pyropia yezoensis (Rhodophyta) using ITS and cox1 markers. Algae 30:217-222. https://doi.org/10.4490/algae.2015.30.3.217
  28. Lee, S. J., Jee, B. Y., Son, M. -H. & Lee, S. -R. 2017. Infection and cox2 sequence of Pythium chondricola (Oomycetes) causing red rot disease in Pyropia yezoensis (Rhodophyta) in Korea. Algae 32:155-160. https://doi.org/10.4490/algae.2017.32.5.16
  29. Levesque, C. A., Brouwer, H., Cano, L., Hamilton, J. P., Holt, C., Huitema, E., Raffaele, S., Robideau, G. P., Thines, M., Win, J., Zerillo, M. M., Beakes, G. W., Boore, J. L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S. I., Gachon, C. M. M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R. H. Y., Johnson, J., Krajaejun, T., Lin, H., Meijer, H. J. G., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Shetty, J., Stajich, J. E., Tripathy, S., Wawra, S., van West, P., Whitty, B. R., Coutinho, P. M., Henrissat, B., Martin, F., Thomas, P. D., Tyler, B. M., De Vries, R. P., Kamoun, S., Yandell, M., Tisserat, N. & Buell, C. R. 2010. Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire. Genome Biol. 11:R73. https://doi.org/10.1186/gb-2010-11-7-r73
  30. Levesque, C. A. & de Cock, A. W. A. M. 2004. Molecular phylogeny and taxonomy of the genus Pythium. Mycol. Res. 108:1363-1383. https://doi.org/10.1017/S0953756204001431
  31. McGowan, J. & Fitzpatrick, D. A. 2017. Genomic, network, and phylogenetic analysis of the oomycete effector arsenal. mSphere 2:e00408-17.
  32. Min, X. J., Butler, G., Storms, R. & Tsang, A. 2005. OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res. 33:W677-W680. https://doi.org/10.1093/nar/gki394
  33. Morgan, W. & Kamoun, S. 2007. RXLR effectors of plant pathogenic oomycetes. Curr. Opin. Microbiol. 10:332-338. https://doi.org/10.1016/j.mib.2007.04.005
  34. Mukai, L. S., Craigie, J. S. & Brown, R. G. 1981. Chemical composition and structure of the cell walls of the conchocelis and thallus phases of Porphyra tenera (Rhodophyceae). J. Phycol. 17:192-198. https://doi.org/10.1111/j.0022-3646.1981.00192.x
  35. Petsalaki, E. I., Bagos, P. G., Litou, Z. I. & Hamodrakas, S. J. 2006. PredSL: a tool for the N-terminal sequence-based prediction of protein subcellular localization. Genomics Proteomics Bioinformatics 4:48-55. https://doi.org/10.1016/S1672-0229(06)60016-8
  36. Promponas, V. J., Enright, A. J., Tsoka, S., Kreil, D. P., Leroy, C., Hamodrakas, S., Sander, C. & Ouzounis, C. A. 2000. CAST: an iterative algorithm for the complexity analysis of sequence tracts. Bioinformatics 16:915-922. https://doi.org/10.1093/bioinformatics/16.10.915
  37. Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., Heger, A., Holm, L., Sonnhammer, E. L. L., Eddy, S. R., Bateman, A. & Finn, R. D. 2012. The Pfam protein families database. Nucleic Acids Res. 40:D290-D301. https://doi.org/10.1093/nar/gkr1065
  38. Qiu, L., Mao, Y., Tang, L., Tang, X. & Mo, Z. 2019. Characterization of Pythium chondricola associated with red rot disease of Pyropia yezoensis (Ueda) (Bangiales, Rhodophyta) from Lianyungang, China. J. Oceanol. Limnol. 37:1102-1112. https://doi.org/10.1007/s00343-019-8075-3
  39. Saunders, D. G. O., Win, J., Cano, L. M., Szabo, L. J., Kamoun, S. & Raffaele, S. 2012. Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi. PLoS ONE 7:e29847. https://doi.org/10.1371/journal.pone.0029847
  40. Savory, F. R., Milner, D. S., Miles, D. C. & Richards, T. A. 2018. Ancestral function and diversification of a horizontally acquired oomycete carboxylic acid transporter. Mol. Biol. Evol. 35:1887-1900. https://doi.org/10.1093/molbev/msy082
  41. Schultz-Johansen, M., Bech, P. K., Hennessy, R. C., Glaring, M. A., Barbeyron, T., Czjzek, M. & Stougaard, P. 2018. A novel enzyme portfolio for red algal polysaccharide degradation in the marine bacterium Paraglaciecola hydrolytica S66T encoded in a sizeable polysaccharide utilization locus. Front. Microbiol. 9:839. https://doi.org/10.3389/fmicb.2018.00839
  42. Simao, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. & Zdobnov, E. M. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210-3212. https://doi.org/10.1093/bioinformatics/btv351
  43. Sparrow, F. K. 1931. Two new species of Pythium parasitic on green algae. Ann. Bot. 45:257-277. https://doi.org/10.1093/oxfordjournals.aob.a090275
  44. Sun, F., Kale, S. D., Azurmendi, H. F., Li, D., Tyler, B. M. & Capelluto, D. G. S. 2013. Structural basis for interactions of the Phytophthora sojae RxLR effector Avh5 with phosphatidylinositol 3-phosphate and for host cell entry. Mol. Plant-Microbe Interact. 26:330-344. https://doi.org/10.1094/MPMI-07-12-0184-R
  45. Tyler, B. M., Tripathy, S., Zhang, X., Dehal, P., Jiang, R. H. Y., Aerts, A., Arredondo, F. D., Baxter, L., Bensasson, D., Beynon, J. L., Chapman, J., Damasceno, C. M. B., Dorrance, A. E., Dou, D., Dickerman, A. W., Dubchak, I. L., Garbelotto, M., Gijzen, M., Gordon, S. G., Govers, F., Grunwald, N. J., Huang, W., Ivors, K. L., Jones, R. W., Kamoun, S., Krampis, K., Lamour, K. H., Lee, M. -K., McDonald, W. H., Medina, M., Meijer, H. J. G., Nordberg, E. K., Maclean, D. J., Ospina-Giraldo, M. D., Morris, P. F., Phuntumart, V., Putnam, N. H., Rash, S., Rose, J. K. C., Sakihama, Y., Salamov, A. A., Savidor, A., Scheuring, C. F., Smith, B. M., Sobral, B. W. S., Terry, A., Torto-Alalibo, T. A., Win, J., Xu, Z., Zhang, H., Grigoriev, I. V., Rokhsar, D. S. & Boore, J. L. 2006. Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis. Science 313:1261-1266. https://doi.org/10.1126/science.1128796
  46. Van der Plaats-Niterink, A. J. 1981. Monograph of the genus Pythium. Stud. Mycol. 21:1-244.
  47. Wawra, S., Trusch, F., Matena, A., Apostolakis, K., Linne, U., Zhukov, I., Stanek, J., Kozminski, W., Davidson, I., Secombes, C. J., Bayer, P. & van West, P. 2017. The RxLR motif of the host targeting effector AVR3a of Phytophthora infestans is cleaved before secretion. Plant Cell 29:1184-1195. https://doi.org/10.1105/tpc.16.00552